ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1887A>G (p.Ile629Met)

dbSNP: rs1583314135
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV001013542 SCV001174144 uncertain significance Hereditary cancer-predisposing syndrome 2022-04-26 criteria provided, single submitter clinical testing The p.I629M variant (also known as c.1887A>G), located in coding exon 11 of the PMS2 gene, results from an A to G substitution at nucleotide position 1887. The isoleucine at codon 629 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species, and methionine is the reference amino acid in other vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV001013542 SCV002052914 uncertain significance Hereditary cancer-predisposing syndrome 2021-04-20 criteria provided, single submitter clinical testing This missense variant replaces isoleucine with methionine at codon 629 of the PMS2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Invitae RCV001860742 SCV002232322 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2021-11-15 criteria provided, single submitter clinical testing Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PMS2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 820259). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 629 of the PMS2 protein (p.Ile629Met).

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